I think it would be better if they had both died.
Tony didn't die. After the gangs took him away, they discovered that he was still alive and they dug the bullet out with their switch knives. Everyone was so overjoyed they danced through the streets and into the subway where they were run down by a train on its way to The Bronx.
Tony ran to Doc's candy store to tell him about plans to marry Maria. Doc told him that
Maria had been so distraught she had thrown herself off the Chrysler Building.
So, Tony married Doc instead.
Man! You just can't beat those adaptations of Shakespeare.
And This, Too, Shall Pass Away

I get annoyed by inaccuracies of realism in films that are aiming to be mostly realistic, but that doesn't apply to a film like WSS which is clearly an allegorical / symbolic / dramatic interpretation of reality. People don't usually burst into group song every five minutes either

This:
I think the OP was concerned that in the real world the police wouldn't have allowed any such tampering with the crime scene
is entirely possible, but who knows?

FOF, I agree that the ending makes dramatic sense. I think the OP was concerned that in the real world the police wouldn't have allowed any such tampering with the crime scene.

I see absolutely nothing wrong with the fact that several Jets and Sharks came together to carry Tony's body off after he'd been shot and killed by Chino. In fact, it proved that intergroup reconciliation, as difficult as it often is, still has the possibility to develop.

I don't know where you got this from, but you are wrong. The ending of the show is exactly the same as the film. Maria does not kill herself.
Let Zygons be Zygons

The movie starts with two gangs dancing through the streets of NY and you only became concerned about lack of realism at the end?
As is noted elsewhere, the original stage musical had Maria committing suicide at the end. That scene was removed because it was felt that it made the play too dark. I doubt that either the play or the movie would have been as successful with such an ending.